Relative abundance of unmapped is negative

[LukCR]

Hi,
Thanks in advance for this amazing tool. I am using coverm to calculate the relative abundance of my MAGs.

I am running into something that confused me a bit, the command I used was this:

coverm genome -b 13.mapped.bam -d dereplicated_genomes/rename13 -x fa -o bin_abund_13.tsv -m relative_abundance

The log for this is the following:

[2025-06-29T00:06:29Z INFO coverm::genome] Of 4085 reference IDs, 3556 were assigned to a genome and 529 were not
[2025-06-29T00:11:58Z INFO coverm::genome] In sample '13.mapped', found 23188520 reads mapped out of 20083103 total (115.46%)

What confused me was the fact that there were more reads found than the total of reads. Then in the tsv file, I got this:

Genome 13.mapped Relative Abundance (%)
unmapped -15.462828
Nuevo13.bin.1.10 1.9023643
Nuevo13.bin.1.103 0.6393372

I noticed the negative value is the same excedent from the reads found, (-15.46%, 115.46%).

Is this due to a mistake I made in the mapping? or is normal

[wwood]

Hi @LukCR

I've not come across this situation before. I suspect it has something to do with your BAM file. Would you mind posting a samtools stats of it? How was it created?

Thanks, ben

[LukCR]

Hi @wwood, thanks for the response.

The BAM file was created with:

samtools fastq /bams/M313.PAU32004.mod.resume1.bam -T MM,ML | minimap2 --secondary=no -ax map-ont -y /dereplicated_genomes/drep_ref_names.fna -|
samtools view -b | samtools sort -o /home/M313.mapped.bam

link to the output of samtools stats:
https://drive.google.com/drive/folders/1GLZ0JMrdEslTE5YBHgU-wq8HfXRldVgR

the header of the file:

[lcasanova@toki-hm-4 tag_reads]$ head stats.out -n 50
This file was produced by samtools stats (1.21+htslib-1.21) and can be plotted using plot-bamstats
This file contains statistics for all reads.
The command line was: stats -@ 30 M313.mapped.bam
CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK f9c4b247 baaeed61 d1d16662
Summary Numbers. Use grep ^SN | cut -f 2- to extract this part.
SN raw total sequences: 20083103 # excluding supplementary and secondary reads
SN filtered sequences: 0
SN sequences: 20083103
SN is sorted: 1
SN 1st fragments: 20083103
SN last fragments: 0
SN reads mapped: 18914948
SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
SN reads unmapped: 1168155
SN reads properly paired: 0 # proper-pair bit set
SN reads paired: 0 # paired-end technology bit set
SN reads duplicated: 0 # PCR or optical duplicate bit set
SN reads MQ0: 182652 # mapped and MQ=0
SN reads QC failed: 0
SN non-primary alignments: 0
SN supplementary alignments: 10769274
SN total length: 130316735481 # ignores clipping
SN total first fragment length: 130316735481 # ignores clipping
SN total last fragment length: 0 # ignores clipping
SN bases mapped: 126018078075 # ignores clipping
SN bases mapped (cigar): 111735759764 # more accurate
SN bases trimmed: 0
SN bases duplicated: 0
SN mismatches: 9286554675 # from NM fields
SN error rate: 8.311175e-02 # mismatches / bases mapped (cigar)
SN average length: 6489
SN average first fragment length: 6489
SN average last fragment length: 0
SN maximum length: 3486436
SN maximum first fragment length: 3486436
SN maximum last fragment length: 0
SN average quality: 33.5
SN insert size average: 0.0
SN insert size standard deviation: 0.0
SN inward oriented pairs: 0
SN outward oriented pairs: 0
SN pairs with other orientation: 0
SN pairs on different chromosomes: 0
SN percentage of properly paired reads (%): 0.0
First Fragment Qualities. Use grep ^FFQ | cut -f 2- to extract this part.
Columns correspond to qualities and rows to cycles. First column is the cycle number.
FFQ 1 0 0 444258 2492985 1496789 768601 497762 389759 350611 300388 257618 227352 205258 191379 182825 178688 177681 180222 185830 194796 205109 219186 230821 253279 270227 288107 305740 327410 354732 376191 405644 445826 470331 494310 562199 609443 540207 621868 793452 721906 553479 424716 339981 267390 223774 177957 123605 86026 58897 40872 567616 0